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Unusually Fast bis-Histidyl Coordination in a Plant Hemoglobin. Int J Mol Sci 2021; 22:ijms22052740. [PMID: 33800498 PMCID: PMC7962945 DOI: 10.3390/ijms22052740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/16/2021] [Accepted: 03/02/2021] [Indexed: 11/17/2022] Open
Abstract
The recently identified nonsymbiotic hemoglobin gene MtGlb1-2 of the legume Medicago truncatula possesses unique properties as it generates four alternative splice forms encoding proteins with one or two heme domains. Here we investigate the ligand binding kinetics of MtGlb1-2.1 and MtGlb1-2.4, bearing two hemes and one heme, respectively. Unexpectedly, the overall time-course of ligand rebinding was unusually fast. Thus, we complemented nanosecond laser flash photolysis kinetics with data collected with a hybrid femtosecond–nanosecond pump–probe setup. Most photodissociated ligands are rebound geminately within a few nanoseconds, which leads to rates of the bimolecular rebinding to pentacoordinate species in the 108 M−1s−1 range. Binding of the distal histidine to the heme competes with CO rebinding with extremely high rates (kh ~ 105 s−1). Histidine dissociation from the heme occurs with comparable rates, thus resulting in moderate equilibrium binding constants (KH ~ 1). The rate constants for ligation and deligation of distal histidine to the heme are the highest reported for any plant or vertebrate globin. The combination of microscopic rates results in unusually high overall ligand binding rate constants, a fact that contributes to explaining at the mechanistic level the extremely high reactivity of these proteins toward the physiological ligands oxygen, nitric oxide and nitrite.
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Mycobacterial and Human Ferrous Nitrobindins: Spectroscopic and Reactivity Properties. Int J Mol Sci 2021; 22:ijms22041674. [PMID: 33562340 PMCID: PMC7915275 DOI: 10.3390/ijms22041674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 12/24/2022] Open
Abstract
Structural and functional properties of ferrous Mycobacterium tuberculosis (Mt-Nb) and human (Hs-Nb) nitrobindins (Nbs) were investigated. At pH 7.0 and 25.0 °C, the unliganded Fe(II) species is penta-coordinated and unlike most other hemoproteins no pH-dependence of its coordination was detected over the pH range between 2.2 and 7.0. Further, despite a very open distal side of the heme pocket (as also indicated by the vanishingly small geminate recombination of CO for both Nbs), which exposes the heme pocket to the bulk solvent, their reactivity toward ligands, such as CO and NO, is significantly slower than in most hemoproteins, envisaging either a proximal barrier for ligand binding and/or crowding of H2O molecules in the distal side of the heme pocket which impairs ligand binding to the heme Fe-atom. On the other hand, liganded species display already at pH 7.0 and 25 °C a severe weakening (in the case of CO) and a cleavage (in the case of NO) of the proximal Fe-His bond, suggesting that the ligand-linked movement of the Fe(II) atom onto the heme plane brings about a marked lengthening of the proximal Fe-imidazole bond, eventually leading to its rupture. This structural evidence is accompanied by a marked enhancement of both ligands dissociation rate constants. As a whole, these data clearly indicate that structural–functional relationships in Nbs strongly differ from what observed in mammalian and truncated hemoproteins, suggesting that Nbs play a functional role clearly distinct from other eukaryotic and prokaryotic hemoproteins.
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NO Scavenging through Reductive Nitrosylation of Ferric Mycobacterium tuberculosis and Homo sapiens Nitrobindins. Int J Mol Sci 2020; 21:ijms21249395. [PMID: 33321752 PMCID: PMC7763097 DOI: 10.3390/ijms21249395] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/24/2020] [Accepted: 12/01/2020] [Indexed: 11/17/2022] Open
Abstract
Ferric nitrobindins (Nbs) selectively bind NO and catalyze the conversion of peroxynitrite to nitrate. In this study, we show that NO scavenging occurs through the reductive nitrosylation of ferric Mycobacterium tuberculosis and Homo sapiens nitrobindins (Mt-Nb(III) and Hs-Nb(III), respectively). The conversion of Mt-Nb(III) and Hs-Nb(III) to Mt-Nb(II)-NO and Hs-Nb(II)-NO, respectively, is a monophasic process, suggesting that over the explored NO concentration range (between 2.5 × 10−5 and 1.0 × 10−3 M), NO binding is lost in the mixing time (i.e., NOkon ≥ 1.0 × 106 M−1 s−1). The pseudo-first-order rate constant for the reductive nitrosylation of Mt-Nb(III) and Hs-Nb(III) (i.e., k) is not linearly dependent on the NO concentration but tends to level off, with a rate-limiting step (i.e., klim) whose values increase linearly with [OH−]. This indicates that the conversion of Mt-Nb(III) and Hs-Nb(III) to Mt-Nb(II)-NO and Hs-Nb(II)-NO, respectively, is limited by the OH−-based catalysis. From the dependence of klim on [OH−], the values of the second-order rate constant kOH− for the reductive nitrosylation of Mt-Nb(III)-NO and Hs-Nb(III)-NO were obtained (4.9 (±0.5) × 103 M−1 s−1 and 6.9 (±0.8) × 103 M−1 s−1, respectively). This process leads to the inactivation of two NO molecules: one being converted to HNO2 and another being tightly bound to the ferrous heme-Fe(II) atom.
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Bozhanova NG, Calcutt MW, Beavers WN, Brown BP, Skaar EP, Meiler J. Lipocalin Blc is a potential heme-binding protein. FEBS Lett 2020; 595:206-219. [PMID: 33210733 PMCID: PMC8177097 DOI: 10.1002/1873-3468.14001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 11/09/2022]
Abstract
Lipocalins are a superfamily of functionally diverse proteins defined by a well-conserved tertiary structure despite variation in sequence. Lipocalins bind and transport small hydrophobic molecules in organisms of all kingdoms. However, there is still uncertainty regarding the function of some members of the family, including bacterial lipocalin Blc from Escherichia coli. Here, we present evidence that lipocalin Blc may be involved in heme binding, trans-periplasmic transport, or heme storage. This conclusion is supported by a cocrystal structure, mass-spectrometric data, absorption titration, and in silico analysis. Binding of heme is observed at low micromolar range with one-to-one ligand-to-protein stoichiometry. However, the absence of classical coordination to the iron atom leaves the possibility that the primary ligand of Blc is another tetrapyrrole.
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Affiliation(s)
- Nina G Bozhanova
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - M Wade Calcutt
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - William N Beavers
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Benjamin P Brown
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.,Institute for Drug Discovery, Medical School, Leipzig University, Germany
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Abbruzzetti S, Allegri A, Bidon-Chanal A, Ogata H, Soavi G, Cerullo G, Bruno S, Montali C, Luque FJ, Viappiani C. Electrostatic Tuning of the Ligand Binding Mechanism by Glu27 in Nitrophorin 7. Sci Rep 2018; 8:10855. [PMID: 30022039 PMCID: PMC6052033 DOI: 10.1038/s41598-018-29182-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/02/2018] [Indexed: 12/29/2022] Open
Abstract
Nitrophorins (NP) 1-7 are NO-carrying heme proteins found in the saliva of the blood-sucking insect Rhodnius prolixus. The isoform NP7 displays peculiar properties, such as an abnormally high isoelectric point, the ability to bind negatively charged membranes, and a strong pH sensitivity of NO affinity. A unique trait of NP7 is the presence of Glu in position 27, which is occupied by Val in other NPs. Glu27 appears to be important for tuning the heme properties, but its influence on the pH-dependent NO release mechanism, which is assisted by a conformational change in the AB loop, remains unexplored. Here, in order to gain insight into the functional role of Glu27, we examine the effect of Glu27 → Val and Glu27 → Gln mutations on the ligand binding kinetics using CO as a model. The results reveal that annihilation of the negative charge of Glu27 upon mutation reduces the pH sensitivity of the ligand binding rate, a process that in turn depends on the ionization of Asp32. We propose that Glu27 exerts a through-space electrostatic action on Asp32, which shifts the pKa of the latter amino acid towards more acidic values thus reducing the pH sensitivity of the transition between open and closed states.
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Affiliation(s)
- Stefania Abbruzzetti
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43124, Parma, Italy.
| | - Alessandro Allegri
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43124, Parma, Italy
| | - Axel Bidon-Chanal
- Department of Nutrition, Food Sciences and Gastronomy, Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB), University of Barcelona, Avda. Prat de la Riba 171, Santa Coloma de Gramenet, Spain
| | - Hideaki Ogata
- Max-Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470, Mülheim an der Ruhr, Germany.,Institute of Low Temperature Science, Hokkaido University Kita19-Nishi8, Kita-ku, 060-0819, Sapporo, Japan
| | - Giancarlo Soavi
- Cambridge Graphene Centre, University of Cambridge, 9 JJ Thomson Avenue, Cambridge, CB3 OFA, UK
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy
| | - Stefano Bruno
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, 43124, Parma, Italy
| | - Chiara Montali
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43124, Parma, Italy
| | - F Javier Luque
- Department of Nutrition, Food Sciences and Gastronomy, Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB), University of Barcelona, Avda. Prat de la Riba 171, Santa Coloma de Gramenet, Spain.
| | - Cristiano Viappiani
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43124, Parma, Italy.
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He C, Ogata H, Lubitz W. Elucidation of the heme active site electronic structure affecting the unprecedented nitrite dismutase activity of the ferriheme b proteins, the nitrophorins. Chem Sci 2016; 7:5332-5340. [PMID: 30155185 PMCID: PMC6020753 DOI: 10.1039/c6sc01019a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/23/2016] [Indexed: 12/14/2022] Open
Abstract
Nitrophorins (NPs) catalyze the nitrite dismutation reaction that is unprecedented in ferriheme proteins. Despite progress in studying the reaction mechanism, fundamental issues regarding the correlation of the structural features with the nitrite dismutase activity of NPs remain elusive. On the other hand, it has been shown that the nitrite complexes of NPs are unique among those of the ferriheme proteins since some of their electron paramagnetic resonance (EPR) spectra show significant highly anisotropic low spin (HALS) signals with large gmax values over 3.2. The origin of HALS signals in ferriheme proteins or models is not well understood, especially in cases where axial ligands other than histidine are present. In this study several mutations were introduced in NP4. The related nitrite coordination and dismutation reaction were investigated. As a result, the EPR spectra of the NP-nitrite complexes were found to be tightly correlated with the extent of heme ruffling and protonation state of the proximal His ligand-dictated by an extended H-bonding network at the heme active site. Furthermore, it is established that the two factors are essential in determining the nitrite dismutase activity of NPs. These results may provide a valuable guide for identifying or designing novel heme proteins with similar activity.
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Affiliation(s)
- Chunmao He
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , D-45470 , Mülheim an der Ruhr , Germany . ;
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , D-45470 , Mülheim an der Ruhr , Germany . ;
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , D-45470 , Mülheim an der Ruhr , Germany . ;
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Knipp M, Ogata H, Soavi G, Cerullo G, Allegri A, Abbruzzetti S, Bruno S, Viappiani C, Bidon-Chanal A, Luque FJ. Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7. F1000Res 2015; 4:45. [PMID: 26167269 PMCID: PMC4482215 DOI: 10.12688/f1000research.6060.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/28/2015] [Indexed: 11/20/2022] Open
Abstract
Nitrophorins represent a unique class of heme proteins that are able to perform the delicate transportation and release of the free-radical gaseous messenger nitric oxide (NO) in a pH-triggered manner. Besides its ability to bind to phospholipid membranes, the N-terminus contains an additional Leu-Pro-Gly stretch, which is a unique sequence trait, and the heme cavity is significantly altered with respect to other nitrophorins. These distinctive features encouraged us to solve the X-ray crystallographic structures of NP7 at low and high pH and bound with different heme ligands (nitric oxide, histamine, imidazole). The overall fold of the lipocalin motif is well preserved in the different X-ray structures and resembles the fold of other nitrophorins. However, a chain-like arrangement in the crystal lattice due to a number of head-to-tail electrostatic stabilizing interactions is found in NP7. Furthermore, the X-ray structures also reveal ligand-dependent changes in the orientation of the heme, as well as in specific interactions between the A-B and G-H loops, which are considered to be relevant for the biological function of nitrophorins. Fast and ultrafast laser triggered ligand rebinding experiments demonstrate the pH-dependent ligand migration within the cavities and the exit route. Finally, the topological distribution of pockets located around the heme as well as from inner cavities present at the rear of the protein provides a distinctive feature in NP7, so that while a loop gated exit mechanism to the solvent has been proposed for most nitrophorins, a more complex mechanism that involves several interconnected gas hosting cavities is proposed for NP7.
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Affiliation(s)
- Markus Knipp
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr, 45470, Germany
| | - Hideaki Ogata
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr, 45470, Germany
| | - Giancarlo Soavi
- Dipartimento di Fisica, Politecnico di Milano, Milano, 20133, Italy
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano, Milano, 20133, Italy
| | - Alessandro Allegri
- Dipartimento di Fisica e Scienze della Terra, Università di Parma, Parma, 43124, Italy
| | - Stefania Abbruzzetti
- Dipartimento di Bioscienze, Università di Parma, Parma, 43124, Italy ; NEST, Istituto Nanoscienze, Consiglio Nazionale delle Ricerche, Pisa, 56127, Italy
| | - Stefano Bruno
- Dipartimento di Farmacia, Università di Parma, Parma, 43124, Italy
| | - Cristiano Viappiani
- Dipartimento di Fisica e Scienze della Terra, Università di Parma, Parma, 43124, Italy ; NEST, Istituto Nanoscienze, Consiglio Nazionale delle Ricerche, Pisa, 56127, Italy
| | - Axel Bidon-Chanal
- Departament de Fisicoquímica, Facultat de Farmàcia and Institute of Biomedicine, Universitat de Barcelona, Santa Coloma de Gramenet, E-08921, Spain
| | - F Javier Luque
- Departament de Fisicoquímica, Facultat de Farmàcia and Institute of Biomedicine, Universitat de Barcelona, Santa Coloma de Gramenet, E-08921, Spain
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